Iron in PDB 7szf: Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound

The structure of Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound, PDB code: 7szf was solved by J.Bridwell-Rabb, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.19 / 1.79
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.73, 96.932, 80.809, 90, 106.97, 90
R / Rfree (%)	15.8 / 19.6

The structure of Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Iron atom in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound (pdb code 7szf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound, PDB code: 7szf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe807 b:19.0 occ:1.00 NE2 A:HIS169 2.0 17.9 1.0 OD1 A:ASP280 2.1 20.9 1.0 NE2 A:HIS164 2.1 22.8 1.0 O A:HOH1050 2.1 20.8 1.0 O A:HOH1045 2.2 26.1 1.0 OD2 A:ASP280 2.4 22.7 1.0 CG A:ASP280 2.6 19.3 1.0 CD2 A:HIS169 3.0 18.1 1.0 CE1 A:HIS169 3.0 17.2 1.0 CD2 A:HIS164 3.1 21.9 1.0 CE1 A:HIS164 3.1 23.8 1.0 ND2 A:ASN158 4.0 17.4 1.0 CB A:ASP280 4.1 18.0 1.0 OD1 A:ASN158 4.1 20.4 1.0 CG A:HIS169 4.1 18.1 1.0 ND1 A:HIS169 4.1 18.2 1.0 ND1 A:HIS164 4.2 23.2 1.0 CG A:HIS164 4.2 18.7 1.0 CD1 A:ILE168 4.3 26.0 1.0 O2 A:D82803 4.4 26.9 1.0 CG1 A:VAL276 4.4 21.2 1.0 CG A:ASN158 4.5 20.8 1.0 O A:ASN158 4.5 18.6 1.0 CE1 A:PHE165 4.5 23.5 1.0 O A:HOH944 4.6 27.0 1.0 C5 A:D82803 4.6 25.4 1.0 CD1 A:PHE165 4.7 20.6 1.0 CG1 A:ILE168 4.7 25.0 1.0 CA A:ASP280 4.8 15.4 1.0 O A:VAL276 4.9 18.0 1.0 C6 A:D82803 5.0 25.2 1.0

Iron binding site 2 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe808 b:22.5 occ:1.00 FE1 A:FES808 0.0 22.5 1.0 S1 A:FES808 2.2 24.7 1.0 ND1 A:HIS77 2.2 23.5 1.0 S2 A:FES808 2.2 21.2 1.0 ND1 A:HIS57 2.3 25.5 1.0 FE2 A:FES808 2.7 22.1 1.0 CG A:HIS77 3.1 23.1 1.0 CG A:HIS57 3.2 26.1 1.0 CE1 A:HIS77 3.2 22.1 1.0 CE1 A:HIS57 3.3 22.4 1.0 CB A:HIS57 3.3 21.4 1.0 CB A:HIS77 3.4 22.4 1.0 N A:HIS77 3.7 25.1 1.0 CB A:TYR76 4.1 20.4 1.0 CA A:HIS77 4.2 25.7 1.0 N A:ARG58 4.2 22.3 1.0 NE2 A:HIS77 4.3 23.6 1.0 CD2 A:HIS77 4.3 22.5 1.0 CD2 A:HIS57 4.3 26.0 1.0 CD2 A:TYR76 4.4 21.9 1.0 NE2 A:HIS57 4.4 22.7 1.0 CB A:ARG58 4.5 28.2 1.0 SG A:CYS55 4.5 23.1 1.0 CG A:TYR76 4.5 20.0 1.0 NE1 A:TRP79 4.6 21.0 1.0 C A:TYR76 4.6 22.0 1.0 SG A:CYS74 4.6 23.6 1.0 CG A:ARG58 4.6 22.6 1.0 CA A:HIS57 4.6 24.4 1.0 CD1 A:TRP79 4.7 22.3 1.0 CE2 A:TRP79 4.7 21.3 1.0 C A:HIS57 4.8 27.7 1.0 CA A:TYR76 4.9 20.6 1.0 CG A:TRP79 4.9 27.8 1.0 CD2 A:TRP79 4.9 25.4 1.0 C A:HIS77 5.0 25.4 1.0 CA A:ARG58 5.0 21.0 1.0

Iron binding site 3 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe808 b:22.1 occ:1.00 FE2 A:FES808 0.0 22.1 1.0 S2 A:FES808 2.2 21.2 1.0 S1 A:FES808 2.2 24.7 1.0 SG A:CYS74 2.4 23.6 1.0 SG A:CYS55 2.4 23.1 1.0 FE1 A:FES808 2.7 22.5 1.0 CB A:CYS55 3.2 21.9 1.0 CB A:CYS74 3.2 22.3 1.0 CB A:HIS57 4.1 21.4 1.0 CB A:TYR76 4.4 20.4 1.0 ND1 A:HIS57 4.6 25.5 1.0 N A:HIS77 4.6 25.1 1.0 CA A:CYS55 4.6 21.0 1.0 ND1 A:HIS77 4.6 23.5 1.0 CA A:CYS74 4.7 23.8 1.0 N A:ARG58 4.8 22.3 1.0 CB A:VAL60 4.8 19.3 1.0 CG A:HIS57 4.8 26.1 1.0 N A:TYR76 4.9 20.9 1.0 C A:CYS55 5.0 18.9 1.0

Iron binding site 4 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:24.6 occ:1.00 FE1 B:FES501 0.0 24.6 1.0 S2 B:FES501 2.2 27.0 1.0 S1 B:FES501 2.2 23.4 1.0 SG B:CYS74 2.4 26.5 1.0 SG B:CYS55 2.4 25.3 1.0 FE2 B:FES501 2.7 24.3 1.0 CB B:CYS74 3.2 24.8 1.0 CB B:CYS55 3.2 22.0 1.0 CB B:HIS57 4.1 21.6 1.0 CB B:TYR76 4.3 20.7 1.0 ND1 B:HIS57 4.5 24.3 1.0 N B:HIS77 4.6 22.5 1.0 CA B:CYS74 4.6 28.4 1.0 CA B:CYS55 4.6 23.6 1.0 CD2 B:HIS77 4.7 22.1 1.0 N B:ARG58 4.8 23.3 1.0 N B:TYR76 4.8 26.7 1.0 CB B:VAL60 4.8 24.1 1.0 CG B:HIS57 4.9 23.7 1.0 C B:CYS74 5.0 25.1 1.0 C B:CYS55 5.0 23.9 1.0

Iron binding site 5 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:24.3 occ:1.00 FE2 B:FES501 0.0 24.3 1.0 S2 B:FES501 2.2 27.0 1.0 S1 B:FES501 2.2 23.4 1.0 ND1 B:HIS57 2.3 24.3 1.0 CD2 B:HIS77 2.3 22.1 1.0 FE1 B:FES501 2.7 24.6 1.0 CG B:HIS77 3.1 24.9 1.0 CG B:HIS57 3.2 23.7 1.0 CE1 B:HIS57 3.3 22.4 1.0 NE2 B:HIS77 3.4 28.6 1.0 CB B:HIS57 3.4 21.6 1.0 CB B:HIS77 3.4 22.6 1.0 N B:HIS77 3.8 22.5 1.0 CB B:TYR76 4.1 20.7 1.0 CA B:HIS77 4.2 23.1 1.0 N B:ARG58 4.2 23.3 1.0 ND1 B:HIS77 4.2 28.9 1.0 CE1 B:HIS77 4.3 21.9 1.0 CD2 B:TYR76 4.4 23.3 1.0 CD2 B:HIS57 4.4 23.2 1.0 NE2 B:HIS57 4.4 25.0 1.0 CB B:ARG58 4.5 23.1 1.0 SG B:CYS55 4.5 25.3 1.0 CG B:TYR76 4.5 22.7 1.0 CG B:ARG58 4.5 21.9 1.0 C B:TYR76 4.6 23.9 1.0 NE1 B:TRP79 4.6 26.5 1.0 SG B:CYS74 4.6 26.5 1.0 CA B:HIS57 4.7 24.2 1.0 CD1 B:TRP79 4.7 25.9 1.0 C B:HIS57 4.8 27.7 1.0 CE2 B:TRP79 4.8 25.4 1.0 CA B:TYR76 4.9 24.9 1.0 CA B:ARG58 4.9 23.4 1.0 CG B:TRP79 5.0 29.8 1.0 CD2 B:TRP79 5.0 24.8 1.0 C B:HIS77 5.0 27.6 1.0

Iron binding site 6 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe507 b:20.8 occ:1.00 O B:HOH693 2.0 23.1 1.0 NE2 B:HIS169 2.0 19.5 1.0 NE2 B:HIS164 2.1 24.5 1.0 OD1 B:ASP280 2.1 21.3 1.0 O B:HOH717 2.2 33.1 1.0 OD2 B:ASP280 2.5 23.2 1.0 CG B:ASP280 2.6 22.3 1.0 CE1 B:HIS164 3.0 29.0 1.0 CD2 B:HIS169 3.0 23.8 1.0 CE1 B:HIS169 3.0 21.3 1.0 CD2 B:HIS164 3.0 21.5 1.0 ND2 B:ASN158 3.9 22.8 1.0 OD1 B:ASN158 4.0 23.5 1.0 CB B:ASP280 4.1 18.2 1.0 ND1 B:HIS164 4.1 28.5 1.0 ND1 B:HIS169 4.1 20.9 1.0 CG B:HIS169 4.1 20.7 1.0 CG B:HIS164 4.2 22.6 1.0 CD1 B:ILE168 4.2 29.7 1.0 O B:ASN158 4.3 22.2 1.0 CG B:ASN158 4.3 21.5 1.0 CG1 B:VAL276 4.5 23.4 0.5 CG1 B:VAL276 4.5 23.4 0.5 O2 B:D82505 4.5 29.5 1.0 O B:HOH651 4.5 30.1 1.0 CE1 B:PHE165 4.6 28.0 1.0 C5 B:D82505 4.6 26.1 1.0 CG1 B:ILE168 4.7 31.2 1.0 CD1 B:PHE165 4.7 21.2 1.0 CA B:ASP280 4.8 19.4 1.0 O B:VAL276 4.9 21.5 0.5 O B:VAL276 4.9 21.5 0.5

Iron binding site 7 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:17.7 occ:1.00 FE1 C:FES501 0.0 17.7 1.0 S2 C:FES501 2.2 19.2 1.0 S1 C:FES501 2.2 18.8 1.0 SG C:CYS74 2.3 17.4 1.0 SG C:CYS55 2.4 18.8 1.0 FE2 C:FES501 2.7 18.5 1.0 CB C:CYS74 3.2 14.5 1.0 CB C:CYS55 3.2 17.9 1.0 CB C:HIS57 4.1 21.6 1.0 CB C:TYR76 4.4 17.3 1.0 ND1 C:HIS57 4.5 19.9 1.0 CA C:CYS74 4.6 16.1 1.0 N C:HIS77 4.6 15.3 1.0 CA C:CYS55 4.6 17.2 1.0 ND1 C:HIS77 4.6 17.5 1.0 CB C:VAL60 4.8 20.9 1.0 CG C:HIS57 4.8 19.7 1.0 N C:ARG58 4.8 18.0 1.0 N C:TYR76 4.9 18.4 1.0

Iron binding site 8 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:18.5 occ:1.00 FE2 C:FES501 0.0 18.5 1.0 S2 C:FES501 2.2 19.2 1.0 S1 C:FES501 2.2 18.8 1.0 ND1 C:HIS77 2.2 17.5 1.0 ND1 C:HIS57 2.3 19.9 1.0 FE1 C:FES501 2.7 17.7 1.0 CE1 C:HIS77 3.1 20.0 1.0 CG C:HIS57 3.2 19.7 1.0 CG C:HIS77 3.2 17.9 1.0 CE1 C:HIS57 3.3 19.5 1.0 CB C:HIS57 3.4 21.6 1.0 CB C:HIS77 3.5 19.1 1.0 N C:HIS77 3.8 15.3 1.0 CB C:TYR76 4.1 17.3 1.0 CA C:HIS77 4.2 16.4 1.0 NE2 C:HIS77 4.2 19.1 1.0 N C:ARG58 4.3 18.0 1.0 CD2 C:HIS77 4.3 18.0 1.0 CD2 C:HIS57 4.3 19.5 1.0 NE2 C:HIS57 4.4 20.5 1.0 CD2 C:TYR76 4.4 19.7 1.0 SG C:CYS55 4.5 18.8 1.0 CG C:ARG58 4.5 21.0 1.0 SG C:CYS74 4.5 17.4 1.0 CB C:ARG58 4.5 19.9 1.0 CG C:TYR76 4.6 16.3 1.0 NE1 C:TRP79 4.6 16.6 1.0 C C:TYR76 4.6 17.6 1.0 CA C:HIS57 4.7 19.2 1.0 CE2 C:TRP79 4.7 20.0 1.0 CD1 C:TRP79 4.7 16.0 1.0 C C:HIS57 4.8 21.1 1.0 CA C:TYR76 4.9 18.7 1.0 CG C:TRP79 5.0 17.1 1.0 CD2 C:TRP79 5.0 18.6 1.0

Iron binding site 9 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of the Rieske Non-Heme Iron Oxygenase Gxta with Beta- Saxitoxinol Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe508 b:22.9 occ:1.00 NE2 C:HIS164 2.0 22.0 1.0 O C:HOH737 2.0 32.1 1.0 NE2 C:HIS169 2.0 24.0 1.0 OD1 C:ASP280 2.1 22.3 1.0 O C:HOH750 2.1 25.1 1.0 OD2 C:ASP280 2.3 25.4 1.0 CG C:ASP280 2.5 23.0 1.0 CE1 C:HIS164 2.9 26.2 1.0 CD2 C:HIS169 3.0 27.7 1.0 CE1 C:HIS169 3.0 23.9 1.0 CD2 C:HIS164 3.1 24.4 1.0 CB C:ASP280 4.0 23.4 1.0 ND1 C:HIS164 4.0 26.7 1.0 ND2 C:ASN158 4.1 19.9 1.0 OD1 C:ASN158 4.1 22.6 1.0 ND1 C:HIS169 4.1 23.8 1.0 CG C:HIS164 4.1 21.9 1.0 CG C:HIS169 4.1 29.1 1.0 CG1 C:VAL276 4.4 25.3 1.0 CD1 C:ILE168 4.4 33.3 1.0 O C:HOH652 4.4 30.6 1.0 CG C:ASN158 4.4 26.7 1.0 CE1 C:PHE165 4.5 27.0 1.0 O2 C:D82504 4.5 31.0 1.0 O C:ASN158 4.5 23.2 1.0 C5 C:D82504 4.6 30.3 1.0 CD1 C:PHE165 4.7 26.3 1.0 CA C:ASP280 4.8 20.9 1.0 CG1 C:ILE168 4.8 29.9 1.0 O C:VAL276 4.9 20.5 1.0

J.Liu, J.Tian, C.Perry, A.L.Lukowski, T.I.Doukov, A.R.H.Narayan, J.Bridwell-Rabb. Design Principles For Site-Selective Hydroxylation By A Rieske Oxygenase. Nat Commun V. 13 255 2022.
ISSN: ESSN 2041-1723
PubMed: 35017498
DOI: 10.1038/S41467-021-27822-3